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johnomics@gmail.com

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Technical Skills

Programming: R, Python, JavaScript, SQL, Perl, C.

Engineering: AWS, Nextflow, Docker, Git, CI/CD, Linux.

Bioinformatics: DNA and RNA sequencing analysis, methylation, metabolomics, genome assembly and annotation.

Data analysis: tidyverse, tidymodels, scikit-learn, plotly, D3.

Disclaimer

Made with the R package pagedown based on Nick Strayer’s template.

Last updated on 2025-03-23.

Main

John Davey

A data scientist and software engineer with two decades of bioinformatics experience, delivering robust results efficiently to clients large and small.

Experience

Principal Bioinformatician

Fios Genomics

Remote

present - 2023

  • Built Target Triage and other data mining packages, gathering and synthesising public data automatically for analysis reports to help clients select drug targets faster.
  • Maintained and contributed to core code base of R, SQL and Javascript with Docker / Git / CI/CD.
  • Set up and ran technical skills discussion group for Operations team to share expertise and consider policy choices.

Bioinformatics Team Leader

Fios Genomics

Remote

2023 - 2022

  • Managed multiple long-running data analysis projects with large corporate clients in flexible teams of two to six analysts, including oncology clinical trials, proteomics, metabolomics and DNA/RNA sequencing. Also line managed a team of three analysts.

Senior Bioinformatician

Fios Genomics

Remote

2022 - 2021

  • Delivered analysis reports for many different clients, involving machine learning models (elastic net, random forest, other regression and classification techniques) and many bioinformatics tools, based on DNA and RNA sequencing (Illumina, PacBio, Oxford Nanopore), methylation and other data sources.

Bioinformatician

Bioscience Technology Facility, Department of Biology

University of York

2021 - 2016

  • Collaborated with a majority of the 70+ labs in the deparment on many kinds of data analysis projects, such as:
  • Tapestry, a tool to visualise, edit and report on complete long read assemblies of small eukaryotic genomes (see end-to-end Oxford Nanopore assembly of Angomonas deanei).
  • Cluster analysis of RNA-sequencing time course data with scikit-learn to identify effectors of circadian rhythms in Arabidopsis thaliana (Román et al., PNAS, 2021).
  • Taught courses in Python, gene expression and basic single cell analysis.
  • Organised regular bioinformatics meetings and clinics to share expertise throughout the department.

Herchel Smith Postdoctoral Fellow

Professor Chris Jiggins’s lab, Department of Zoology

University of Cambridge

2016 - 2013

  • One of a team of postdoctoral researchers executing an ERC advanced grant on the causes of speciation in Heliconius butterflies. Focussed on genome structure and chromosome inversions, which required developing new techniques for genome assembly (Davey et al., 2017, Davey et al., 2016).
  • Led a team of twenty to design and present an exhibit on butterfly speciation for the Royal Society Summer Science Exhibition in 2014.

Postdoctoral Bioinformatician

Professor Mark Blaxter’s lab, Institute of Evolutionary Biology

University of Edinburgh

2012 - 2008

Software Engineer

N/A

N/A

2004 - 2002

Worked as a tester and developer on a large C codebase with Oracle SQL database (ask for details).

Education

Ph.D., Neuroinformatics

N/A

University of Edinburgh

2008 - 2005

Thesis title: The Identification of Beta-Catenin and Other RNAs in Developing Thalamic Axons

M. Sc. in Software Engineering

N/A

University of Durham

2001

B. Sc. in Computer Science (1st class Honours)

N/A

University of Durham

1997 - 2000